Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli

Brosius, Jürgen; Dull, Thomas J.; Sleeter, Donald D.; Noller, Harry F.

doi:10.1016/0022-2836(81)90508-8

Cited by 1,646 publications

(888 citation statements)

References 45 publications

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“…PCR amplification of the 16S rDNA fragments prior to DGGE was performed as described by Muyzer et al [23]. The primers targeted eubacterial 16S regions corresponding to Escherichia coli positions 341-534 [2].…”

Section: Dna Extraction and Pcr Amplificationmentioning

confidence: 99%

Utilization of Microbial Biofilms as Monitors of Bioremediation

et al. 2004

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A down-well aquifer microbial sampling system was developed using glass wool or Bio-Sep beads as a solidphase support matrix. Here we describe the use of these devices to monitor the groundwater microbial community dynamics during field bioremediation experiments at the U.S. Department of Energy Natural and Accelerated Bioremediation Research Program's Field Research Center at the Oak Ridge National Laboratory. During the 6-week deployment, microbial biofilms colonized glass wool and bead internal surfaces. Changes in viable biomass, community composition, metabolic status, and respiratory state were reflected in sampler composition, type of donor, and groundwater pH. Biofilms that formed on Bio-Sep beads had 2-13 times greater viable biomass; however, the bead communities were less metabolically active [higher cyclopropane/monoenoic phospholipid fatty acid (PLFA) ratios] and had a lower aerobic respiratory state (lower total respiratory quinone/ PLFA ratio and ubiquinone/menaquinone ratio) than the biofilms formed on glass wool. Anaerobic growth in these systems was characterized by plasmalogen phospholipids and was greater in the wells that received electron donor additions. Partial 16S rDNA sequences indicated that Geobacter and nitrate-reducing organisms were induced by the acetate, ethanol, or glucose additions. DNA and lipid biomarkers were extracted and recovered without the complications that commonly plague sediment samples due to the presence of clay or dissolved organic matter. Although microbial community composition in the groundwater or adjacent sediments may differ from those formed on down-well biofilm samplers, the metabolic activity responses of the biofilms to modifications in groundwater geochemistry record the responses of the microbial community to biostimulation while providing integrative sampling and ease of recovery for biomarker analysis.

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Section: Dna Extraction and Pcr Amplificationmentioning

confidence: 99%

Utilization of Microbial Biofilms as Monitors of Bioremediation

et al. 2004

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“…For the ail-probe, plasmid pVM103 [20] was cut with the restriction enzymes Clal and AvaI according to the manufacturers instruction (Boehringer Mannheim, Rotkreuz, Switzerland), and the fragments were separated by agarose gel electrophoresis. The 1P3 kb Clal-Aval fragment was extracted from the gel [18], and labelled with DIG-dUTP by random priming following the instructions of the manufacturer (Boehringer coli rrnB operon [21] served as template for the rrnprobes. The sequences of the oligonucleotide primers were 5'-AAT GCT GTC TTC ATT TGG-3' and 5'-CGG GAT TGC AAC ATA CAT-3' for the ystprobe [6], and 5'-ATT GAA GAG TTT GAT CAT GGC TCA-3' and 5'-CTC CCA TGG TGT GAC GGG CGG TGT GTA-3' for the 16S and 5'-CTT AGA AGC AGC CAT CAT TT-3' and 5'-CTT TTA TCC GTT GAG CGA TG-3' for the 23S rrn-probes, respectively.…”

Section: Molecular Biology Techniquesmentioning

confidence: 99%

Association between clinical presentation, biogroups and virulence attributes ofYersinia enterocoliticastrains in human diarrhoeal disease

1996

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SummaryTraditionally the enteric pathogenYersinia enterocoliticahas been differentiated into biogroups. Despite being considered as non-pathogenic, biogroup 1A isolates have constituted a sizeable fraction of strains from patients with gastroenteritis in many reports. To establish a potential clinical significance for biogroup 1A isolates ofY. enterocolitica, clinical disease in patients with gastroenteritis excreting such isolates was compared with symptoms among patients found infected with pathogenic biogroups. Clinical data and isolates of 66 patients from whomY. enterocoliticahad been isolated by direct plating were available for study. There was an association between patient age below 3 years and infection with ‘pathogenic’Y. enterocolitica. The severity of gastroenteritis and other symptoms, however, did not depend on the biogroup, or the presence of the virulence plasmid in the yersinia strain isolated from the patients. Strains belonging to biogroup 1A ofY. enterocoliticashowed two clusters of ribotypes, one of which encompassed most isolates recovered from humans, the other being associated with environmental isolates. This might indicate the existence of human-adapted and potentially pathogenic strains among biogroup 1A ofY. enterocolitica.

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“…DNA coding for 16S rRNA regions was amplified by means of PCR with Taq polymerase [13][14][15] . A PCR product for sequencing 16S rDNA regions was prepared by using the following two primers, 20F (5 -GAG TTT GAT CCT GGC TCA G-3 , positions 9-27 on 16S rDNA by the E. coli numbering system) 16 and 1500R (5 -GTT ACC TTG TTA CGA CTT-3 , position 1509-1492 on 16S rDNA by the E. coli numbering system) 16 . The PCR amplification was carried out with DNA Engine Dyad Thermal Cycler (Bio-Rad Laboratories).…”

Section: Pcr Amplification Of 16s Rdnamentioning

confidence: 99%

“…1500 bases, on 16S rDNA by the E. coli numbering system) 16 was carried out. Sequencing of the purified PCR products was carried out with an ABI PRISM BigDye Terminator Ready Reaction Cycle Sequencing Kit (version 3.1, Applied Biosystems, Foster City, California, USA).…”

Section: Direct Sequencing Of 16s Rdnamentioning

confidence: 99%

Identification of phosphate-solubilizing bacteria from the bamboo rhizosphere

Ruangsanka¹

2014

ScienceAsia

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Some bacteria in the root zone of plants can solubilize phosphate making it available to the plant. Bacteria associated with bamboo roots may be a good source for development of bio-fertilizer for organic crop production. Here, 24 soil samples were collected from 8 species of bamboo, and 19 isolates of bacteria with the ability to solubilize phosphate were primarily selected based on the halo-to-colony ratio in Pikovskaya's medium. Five isolates with the highest ratios were cultured in vitro in a liquid medium containing mono-calcium phosphate (Ca(H 2 PO 4 ) 2 ) and soluble phosphate was then determined. The five isolates were identified using the full 16S rDNA sequencing method. Buttiauxella izardii had the highest soluble phosphate (134 mg/l) followed by Enterobacter cancerogenus (110 mg/l), Burkholderia ubonensis (106 mg/l), and E. hormaechei (103 mg/l), whereas Burkholderia pyrrocinia was lowest (38 mg/l). The isolates were further inoculated to soil planted with baby corn (Zea mays) in a pot experiment under an open environment. The experiment was not able to confirm the ability of these bacteria isolates to promote growth of the crop. The potential use of the isolates and the methods to improve the experiments for further studies are discussed.

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Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli

Cited by 1,646 publications

References 45 publications

Utilization of Microbial Biofilms as Monitors of Bioremediation

Utilization of Microbial Biofilms as Monitors of Bioremediation

Association between clinical presentation, biogroups and virulence attributes ofYersinia enterocoliticastrains in human diarrhoeal disease

Identification of phosphate-solubilizing bacteria from the bamboo rhizosphere

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